gatk3的最后一个经典版本3.8

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Eric Banks 83e09b1f64 Created a new walker to do the full combination of N gVCFs from the HC single-sample ref calc pipeline. Basically, it does 3 things (as opposed to having to call into 3 separate walkers): 1. merge the records at any given position into a single one with all alleles and appropriate PLs 2. re-genotype the record using the exact AF calculation model 3. re-annotate the record using the VariantAnnotatorEngine In the course of this work it became clear that we couldn't just use the simpleMerge() method used by CombineVariants; combining HC-based gVCFs is really a complicated process. So I added a new utility method to handle this merging and pulled any related code out of CombineVariants. I tried to clean up a lot of that code, but ultimately that's out of the scope of this project. Added unit tests for correctness testing. Integration tests cannot be used yet because the HC doesn't output correct gVCFs.		2013-12-31 12:07:56 -05:00
licensing	deleted old license files	2013-07-02 16:36:47 -04:00
protected	Created a new walker to do the full combination of N gVCFs from the HC single-sample ref calc pipeline.	2013-12-31 12:07:56 -05:00
public	Created a new walker to do the full combination of N gVCFs from the HC single-sample ref calc pipeline.	2013-12-31 12:07:56 -05:00
settings	Updated the variant jar to grab a bug fix that I made to it	2013-12-17 11:52:34 -05:00
.gitignore	Detect stuck lock-acquisition calls, and disable file locking for tests	2013-04-24 22:49:02 -04:00
README.md	Update README file for the 2.6 release	2013-06-20 13:08:29 -04:00
build.xml	Separate tests that access the knowledge base from other tests	2013-12-06 11:31:35 -05:00
intellij_example.tar.bz2	Removed the intellij files from the root and made an example package for new users. This allows users to start at the same page and then change it as they see fit without interfering with the repo (thanks guillermo!)	2012-09-27 11:04:56 -04:00
ivy.xml	Changing from scala 2.9.2 to 2.10.2.	2013-09-23 12:42:22 -04:00

README.md

The Genome Analysis Toolkit

See http://www.broadinstitute.org/gatk/